- Volume 69, Issue 7, 2019

Two slightly beige-pigmented, Gram-stain-negative, rod-shaped bacterial strains, IMT-291T and IMT-297, were isolated from soil in a field located in Malvern, Alabama, USA. The source soil had been amended with humic acid and continuously used for the cultivation of worms used for fish bait. It is still conceivable that the source of the strains is from the humic acid amendment, although all attempts to isolate the novel phenotypes from the humic acid source have failed. The two strains were identical based on morphology, growth rate and subsequently by 16S rRNA gene sequences, but showed differences in genomic fingerprint patterns generated by rep-PCR. Phylogenetic analysis based on the 16S rRNA gene revealed a placement of the strain in a distinct cluster with Xinfangfangia soli (97.2 % 16S rRNA gene sequence similarity) and in close proximity to the genus Falsirhodobacter with highest 16S rRNA gene sequence similarity of 95.3 % to the type strain of Falsirhodobacter deserti . Sequence similarities to all other type strains were below 95.0 %. The chemotaxonomic analysis showed a clear similarity to the genus Xinfangfangia . The main cellular fatty acids of the strain were C_18 : 1 ω7c, 11-methly-C_18 : 1 ω7c and C_16 : 0. The major quinone was ubiquinone Q-10. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine were predominant in the polar lipid profile. The polyamine pattern contained the major compound spermidine and moderate amounts of putrescine and cadaverine. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. Based on phylogenetic, chemotaxonomic and phenotypic analyses we propose a new species of the genus Xinfangfangia , with the name Xinfangfangia humi sp. nov. and strain IMT-291T (=LMG 30636T=CIP 111625T=CCM 8858T) as type strain.

Three Legionella -like strains, designed km488T, km489 and km521, were isolated from freshwater samples in China. Cells were Gram-stain-negative, rod-shaped and non-spore-forming. Growth was observed on BCYEα agar, but not on BCYEα agar without l-cysteine, chocolate agar with PolyViteX or Columbia blood agar. The major fatty acids (>5 %) of strains km488T, km489 and km521 were C_16 : 0, anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The mip gene sequences (574 nt) showed the isolates were almost identical with more than 99.7 % sequence similarities, and closely matched to L. gormanii ATCC 33297T with 95.4–95.6 % sequence similarities. Phylogenetic analyses based on concatenated gene (16S rRNA, mip, rpoB and rnpB) sequences indicated that the isolates formed a distinct cluster along with L. gormanii within the genus Legionella . Matrix-assisted laser desorption ionization time-of-flight analyses also demonstrated a clear separation between the isolates and other closely and distantly related Legionella species. DNA–DNA hybridization studies demonstrated that the isolates were closely related (92.0 –95.0 % DNA-DNA relatedness) but differentiated from their phylogenetic neighbours (<70 % DNA–DNA relatedness). The whole genome of km488T was sequenced, and showed a G+C content of 37.8 mol%. Based on the findings from this polyphasic taxonomic study, the isolates are considered to represent a single novel species, for which the name Legionella qingyii sp. nov. is proposed. The type strain is km488T (KCTC 15636T=CCTCC AB 2018025T=NRBC 113223T).

In the last 4 years, most of the species previously classified as members of the genus Burkholderia have been transferred to the novel genera Paraburkholderia , Caballeronia , Robbsia , Mycetohabitans and Trinickia . However, there have been objections to splitting the genus Burkholderia sensu lato, and based on this taxonomic opinion, strain RPE64T, which has the 16S rRNA gene sequence identical to that of Caballeronia peredens LMG 29314T, has recently been proposed as the type strain of Burkholderia insecticola sp. nov. The arguments against the split were analysed in this study and found to be not convincing enough to revise the taxonomic positions of members of the novel genera. Therefore, based on the results of phylogenetic analyses, including comparisons of 16S rRNA gene sequences and those of concatenated proteins, as well as on the fact that strain RPE64T had all molecular signatures included as Caballeronia -specific markers in the genus description, we propose to reclassify B. insecticola as Caballeronia insecticola comb. nov. The results of this study also showed that ‘ Burkholderia novacaledonica ’ and ‘ Burkholderia ultramafica ’ should be transferred to the genera Caballeronia and Paraburkholderia , respectively.

A novel blush-red-pigmented, Gram-stain-negative, gliding, aerobic and rod- or oval-shaped bacterium, designated strain 12N15T, was isolated from sediment sampled at a marine saltern located in Wendeng, China (36° 59′ 56.49″ N, 122° 1′ 38.84″ E). Growth was observed at 10–40 °C (optimum, 28 °C), in 1.0–12.0 % NaCl (2.0–5.0 %, w/v) and at pH 6.0–9.5 (pH 7.0). The respiratory quinones were determined to be Q-10 and major fatty acids were C_18 : 1ω7c and C_18 : 0. The polar lipids profile of strain 12N15T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminolipid, phosphatidylcholine, one lipid and three phospholipids. The genomic DNA G+C content was 69.6 mol%. Phylogenetic analyses based on the 16S rRNA gene showed that the strain 12N15T was affiliated within the genus Jannaschia , and was most closely related to Jannaschia seohaensis KCTC 22172T. The average amino acid identity and percentage of conserved protein values between strain 12N15T and the type strain of the type species, Jannaschia helgolandensis DSM 14858T, were 70.2 % and 64.1 %, respectively. The average nucleotide identity value between strain 12N15T and J.annaschia seohaensis KCTC 22172T was 81.9 %. The phenotypic, phylogenetic and genomic analyses supported the hypothesis that strain 12N15T represents a novel species of the genus Jannaschia , for which the name Jannaschia formosa sp. nov. is proposed. The type strain is 12N15T (=MCCC 1H00325T=KCTC 62582T).

A Gram-stain-negative, rod-shaped strain isolated from pig-production environments was identified as a new species within the genus Yersinia using multifaceted genomic and biochemical approaches. The genome of this strain was closed using a hybrid assembly approach combining both high accuracy short read sequencing data with long read sequencing technology. Phylogenetic analysis of the 16S rRNA gene showed ~98 % similarity to Yersinia kristensenii and ~98 % similarity to Yersinia enterocolitica . Average nucleotide identity (OrthoANI) values were calculated as 85.79 % to Y. kristensenii ATCC 33638T and 85.73 % to Y. enterocolitica ATCC 9610T thereby providing evidence that this isolate should be considered as a novel species. The type strain is CFS1934T (=NCTC 14222T=LMG 31076T).

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, designated Hp12T, was isolated from a marine sponge in the intertidal zone off the coast of Seltjarnarnes (64° 16′ N 22° 00′ W), Iceland. Strain Hp12T grew optimally at 20–22 °C, at pH 7–8 and in the presence of 1–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Hp12T in the class Gammaproteobacteria , related to members of the genus Alcanivorax in the order Oceanospirillales with 90.3–88.5 % sequence similarity. The strain had a draft genome size of 4.99 Mbp with a DNA G+C content of 43.0 mol%. Cellular fatty acids were dominated by C_16 : 1 ω7c, C_18 : 1 ω7c and C_16 : 0. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The major respiratory lipoquinones were ubiquinone Q8 and menaquinone MK8. From the taxonomic information and phenotypic properties obtained in this study, it is proposed that strain Hp12T be placed into a novel genus and species named Pelagibaculum spongiae gen. nov., sp. nov. The type strain of Pelagibaculum spongiae is Hp12T (=DSM 104963T=CECT 9367T).

A bacterial strain, designated SODT, with Gram-stain-negative and motile rod-shaped cells, was isolated from soil in Hefei, PR China, and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SODT belonged to the genus Massilia and showed the highest similarities to Massilia violaceinigra B2T (99.3 %), followed by Massilia glaciei B448-2T (98.7 %), Massilia eurypsychrophila CGMCC 1.12828T (98.6 %) and Rugamonas rubra CCM3730T (97.8 %). Average nucleotide identity and digital DNA–DNA hybridization values between genome sequences of strain SODT and the closely related species ranged from 77.1 to 89.3% and from 22.2 to 34.7 %. The DNA G+C content of strain SODT was 65.4 mol%. Strain SODT contained Q-8 as the major ubiquinone and the dominant fatty acids were summed feature 3 (C_16 : 1ω7c and/or C_15 : 0iso 2-OH; 58.5 %), C_16 : 0 (26.8 %) and C_18 : 1ω7c (5.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. On the basis of the evidence presented in this study, strain SODT represents a novel species of the genus Massilia , for which the name Massilia atriviolacea sp. nov. is proposed. The type strain is SODT (=KCTC 62720T=LMG 30840T).

Strain CCP-7T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CCP-7T formed a phylogenetic lineage in the genus Sphingomonas . Strain CCP-7T was most closely related to Sphingomonas starnbergensis 382T and Sphingomonas naphthae DKC-5-1T with 96.2 % 16S rRNA gene sequence similarity. Strain CCP-7T showed 65.5–76.7 % average nucleotide identity and 20.2–22.5 % digital DNA–DNA hybridization identity with the strains of other related Sphingomonas species. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acid of strain CCP-7T was C_18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, three uncharacterized sphingoglycolipids, two uncharacterized phospholipids and six uncharacterized lipids. The predominant polyamine was homospermidine. The only isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CCP-7T was 64.5 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-7T should be classified in a novel species of the genus Sphingomonas , for which the name Sphingomonas crocodyli sp. nov. is proposed. The type strain is CCP-7T (=BCRC 81096T=LMG 30311T=KCTC 62190T).

Three strains of a novel mucoralean fungus were isolated from samples of decayed wood, which were collected from three locations near the city of Chuxiong, Yunnan province, China. These isolates were identified as a novel species through comparison of sequences in the ITS sequence, the D1/D2 domains of the LSU rRNA gene, and other taxonomic characteristics. The results demonstrated that these isolates represent a novel mucoralean fungus species belonging to the genus Mucor. The ITS sequence of Mucor chuxiongensissp. nov. differed from its closest relative, Mucor guilliermondii CBS 174.27T, by 13.1 % sequence divergence (39 substitutions and 38 gaps), and the D1/D2 sequences of the novel strains differed by 13 nt substitutions and one gap (1.9 %) from the ex-type strain. On potato dextrose agar, malt extract agar and synthetic mucor agar, the isolates grew slowly below 10 °C, rapidly at 25–30 °C, and could not grow well at 35 °C. The holotype strain of Mucor chuxiongensis sp. nov. is NYNU 174111 (CICC 41666T=CBS 143707T).

Ten strains representing a single anamorphic novel yeast species were isolated from the external surface (DMKU-SP23 and DMKU-SP40) and tissue (DMKU-SE89, DMKU-SE99, DMKU-SE100 and DMKU-SE147) of sugarcane leaves in Thailand, and phylloplane (IMUFRJR 52034) and rhizoplane (IMUFRJ 52036 and 52037) of sugarcane and associated soil (IMUFRJ 52035) in Brazil. These strains showed zero to two nucleotide substitutions in the sequences of the D1/D2 region of the LSU rRNA gene and zero to three nucleotide substitutions in the internal transcribed spacer (ITS) region. Tremella globispora was the most closely related species, but with 1.7–2.1 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 5.3–6.0 % nucleotide substitutions in the ITS region. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 regions showed that these 10 strains represented a single species belonging to the genus Tremella (class Tremellomycetes, subphylum Agaricomycotina) that was distinct from related species. They therefore represented a novel species of the genus Tremella although the formation of basidia and basidiocarp were not observed. The name Tremella saccharicola f.a., sp. nov. is proposed. The type strain is DMKU-SP23T (=NBRC 109698T=BCC 61186T).

The term ‘standing in nomenclature’ is used in several instances in the International Code of Nomenclature of Prokaryotes, but the term is not defined. An analysis of the way the term has been used in the past and the context in which it is currently used indicates that it may be more appropriate to substitute the term with more suitable wording that is consistent with usage in other parts of the Code.

The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium , Lactobacillus and related organisms was held within the frame of the FoodMicro 2016 Congress in Dublin (FoodMicro 2016, 19–22 July 2016, Dublin, Ireland). The meeting comprised an open session with a workshop entitled ‘Research and networking taxonomy in food with an emphasis on LAB’ and a closed session on issues related to ICSP Subcommittee activities.

Currently, the description of taxa designated Candidatus requires gene sequences and other taxonomically relevant available information in the absence of an isolated pure culture, and Candidatus names are provisional, i.e. without formal standing in nomenclature. If gene sequences are accepted as suitable type material for the description of prokaryotic species, many taxa designated Candidatus would fulfil all the requirements in the International Code of Nomenclature of Prokaryotes for priority. Here we propose that upon acceptance of sequence data as type material, all Candidatus names published before 1 January 2020 which are otherwise in accordance with the rules of the Code will have their priority based upon their date of publication in the International Journal of Systematic and Evolutionary Microbiology, either within a paper, a list of names of Candidatus taxa, or a Validation List, unless a synonymous name already exists based upon deposition of type cultures. We further propose that modifications of the superscript ‘T’ be used to identify the nomenclatural types. If the type material is a culture, the superscript ‘T’ will continue to be used. If the type material is a sequence, the superscript ‘Ts’ will be used. If the type material is some other form of description, the superscript ‘Td’ will be used.